To develop phylodynamic inference and predictive models for Porcine Reproductive and Respiratory Syndrome Virus strains. Closing: 28 November.

We are seeking a highly motivated, quantitative post-doctoral research fellow to develop phylodynamic inference and predictive models for studying the evolution and interaction of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) strains in partially immune swine herds.

About the project:
The study of the ecology and evolution of infectious diseases in animal populations has been greatly enhanced by the use of viral sequence data and temporal-spatial phylodynamic models in recent years. Furthermore, the interactions between co-circulating viral lineages might shape the observed transmission dynamics in the population. This collaborative US-UK project is about ‘landscapes of cross-immunity’ using both transmission experiments and field studies, in the context of the epidemiology and evolution of PRRSV in domestic swine herds.

Your role:
The US project partners will be generating viral genome sequences, and you will use these together with other detailed spatial and immunity related data about the host population to help quantify how cross immunity and population connectivity influence co-circulation using phylodynamic methods by creating, running and parameterising inference and simulation models. Specifically you will integrate immunological / spatial landscapes and networks with the sequence data in a phylodynamic framework (for example by writing an inference package), and simulate different realistic scenarios to compare to the existing data (approximate Bayesian computation model) and to generate predictions for future time periods or under different disease control measures.

About the position:
This post is available at The Roslin Institute under the supervision of Dr Samantha Lycett, Prof Andrea Doeschl-Wilson and Prof Rowland Kao. The Roslin Institute is part of the University of Edinburgh’s College of Medicine and Veterinary Medicine, and is internationally renowned for its multi-disciplinary research in animal health.

The advertised position is part of the US-UK joint NIFA-NSF-NIH-BBSRC Ecology and Evolution of Infectious diseases collaborative project: Drivers of diversity and transmission of co-circulating viral lineages in host meta-populations. The successful candidate will interact with other group members at Roslin and the external US partners from University of Minnesota (US project lead Dr Kim Vanderwaal) from a variety of backgrounds, such as epidemiological modelling, phylodynamics, computational statistics, quantitative and molecular genetics, immunology and animal or veterinary science, and present work to an international audience. Travel to the University of Minnesota for short research visits is also built into the project.

The post-holder must have a PhD in a scientific discipline with a substantial quantitative component (e.g. computational biology, bioinformatics, physics, mathematics, statistics), together with evidence of skills in phylodynamics and/or stochastic individual based modelling (e.g. paper publications or software). Extensive knowledge in at least one programming language is required, scripting for data analysis will also be required; and both Java and R would desirable (because we have existing code/scripts in Java and R). Experience of parallelising code, and high performance or cloud computing would also be desirable. The ideal candidate will have a strong interest in infectious disease dynamics and phylodynamics, be autonomous, organised and collaborative and also possess strong problem solving skills.

The position is full-time (100%) and available for 36 months, with an anticipated starting date of December 2019 or January 2020.

For further information, including details of how to apply, please visit https://www.vacancies.ed.ac.uk/pls/corehrrecruit/erq_jobspec_version_4.display_form

Should you have any informal questions about the project, please contact Samantha Lycett at samantha.lycett@ed.ac.uk